GapMind for catabolism of small carbon sources

 

Alignments for a candidate for pco in Rhodococcus qingshengii djl-6-2

Align acyl-CoA oxidase (EC 1.3.3.6) (characterized)
to candidate WP_024487810.1 C1M55_RS08415 acyl-CoA oxidase

Query= BRENDA::Q33DR0
         (703 letters)



>NCBI__GCF_002893965.1:WP_024487810.1
          Length = 643

 Score =  494 bits (1271), Expect = e-144
 Identities = 272/623 (43%), Positives = 371/623 (59%), Gaps = 2/623 (0%)

Query: 43  GRWADIRLHARDLAGREVVQKVEGLTHTEHRSRVFGQLKYLVDNNAVHRAFPSRLGGSDD 102
           GRW ++R   R     E             RS+   Q++ L D       F    GG+ D
Sbjct: 14  GRWREVRERVRGELNDERFAPHYTPNTAIARSKALEQMRVLADLGYAANGFAVSHGGTGD 73

Query: 103 HGGNIAGFEELVTADPSLQIKAGVQWGLFGSAVMHLGTREHHDKWLPGIMSLEIPGCFAM 162
            GG +   E L  +D SL +KAGVQWGLFG A+ +LGT  HH  ++  ++ L++ GCFAM
Sbjct: 74  AGGAVTSIEMLAMSDLSLMVKAGVQWGLFGGAIENLGTERHHQAYVKPLIDLDLLGCFAM 133

Query: 163 TETGHGSDVASIATTATYDEETQEFVIDTPFRAAWKDYIGNAANDGLAAVVFAQLITRKV 222
           TETGHGSDV  + TTATYD ET EFV+++P  ++ KDYIG AA     A VFAQLIT   
Sbjct: 134 TETGHGSDVQELETTATYDVETGEFVVNSPTPSSRKDYIGGAAQHATVAAVFAQLITGGE 193

Query: 223 NHGVHAFYVDLRDPATGDFLPGIGGEDDGIKGGLNGIDNGRLHFTNVRIPRTNLLNRYGD 282
           + GVH F V +RD A  D LPG+   D G+KGGL G+DNGR+ F  VRIPR NLLNRY D
Sbjct: 194 SQGVHCFVVPIRDDAGND-LPGVTTSDCGLKGGLPGVDNGRIVFDQVRIPRENLLNRYAD 252

Query: 283 VAVDGTYSSTIESPGRRFFTMLGTLVQGRVSLDGAAVAASKVALQSAIHYAAERRQFNAT 342
           VA DGTYSS IE+P RRFFTM+GTLV+GRV++ G+A AA++V L  A  YA +RRQF+A 
Sbjct: 253 VAEDGTYSSAIENPNRRFFTMVGTLVRGRVTVGGSAAAAARVGLAIAGRYALQRRQFSAP 312

Query: 343 SPTEEEVLLDYQRHQRRLFTRLATTYAASFAHEQLLQKFDDVFSGAHDTDADRQDLETLA 402
              +E +++DY  HQ+RL   +A +YA  FA  +L+    D+ S       ++++LE  A
Sbjct: 313 KSDDEVLIMDYLVHQKRLLPLIARSYALQFAQNELVAAMHDIQSSDDPDPQEQRELEGRA 372

Query: 403 AALKPLSTWHALDTLQECREACGGAGFLIENRFASLRADLDVYVTFEGDNTVLLQLVAKR 462
           A LK  +TWHA   +QE REACGGAG+L ENR  +L+AD DV+ TFEGDN VL QLVAK 
Sbjct: 373 AGLKAANTWHATRAIQEAREACGGAGYLAENRLTALKADTDVFTTFEGDNHVLTQLVAKE 432

Query: 463 LLADYAKEFRGANFGVLARYVVDQAAGVALHRTGLRQVAQFVADSGSVQKSALALRDEEG 522
           LL  YA E RG +     R+     + V   RT  +Q+ Q + D+    +   +L +   
Sbjct: 433 LLTSYADEVRGMSPVDWMRFAATTVSDVVKKRTAAQQILQTIVDTRQDNEEDGSLFNRGT 492

Query: 523 QRTLLTDRVQSMVAEVGAALKGAGKLPQHQAAALFNQHQNELIEAAQAHAELLQWEAFTE 582
           Q  +  DR + ++A     L+ A K  ++   A FN  Q+ +++AAQAH E +  EAF  
Sbjct: 493 QMKMFEDREEYLLATAARRLQAAQKREENPFDA-FNFVQDHVLKAAQAHIERVILEAFVA 551

Query: 583 ALAKVDDAGTKEVLTRLRDLFGLSLIEKHLSWYLMNGRLSMQRGRTVGTYINRLLVKIRP 642
            +   +D   KE+   + DL+ LS+IE+  +W++ +  LS++R + V   IN     +RP
Sbjct: 552 GIDSCEDETAKELFGEVCDLYALSVIEEDKAWFMEHRHLSVERSKAVTRGINERCRTLRP 611

Query: 643 HALDLVDAFGYGAEHLRAAIATG 665
           H   L+D FG     L +A+  G
Sbjct: 612 HVETLIDGFGIPDILLGSAMLDG 634


Lambda     K      H
   0.319    0.134    0.387 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 1010
Number of extensions: 45
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 703
Length of database: 643
Length adjustment: 39
Effective length of query: 664
Effective length of database: 604
Effective search space:   401056
Effective search space used:   401056
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 54 (25.4 bits)

This GapMind analysis is from Sep 24 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory